MALDIquant (version 0.5)

labelPeaks-methods: Draws peak labels to plot.

Description

labelPeaks draws the corresponding mass values on top of the peaks stored in a MassPeaks object to a plot.

Usage

## S3 method for class 'MassPeaks':
labelPeaks(object, 
    index,
    mass, massTolerance=0.001,
    digits=3, underline=TRUE, 
    verticalOffset=max(object@intensity)/200, 
    adj=c(0.5, 0), cex=0.7, family="sans", 
    ...)

Arguments

object

MassPeaks object.

index

vector, indices of peaks to label.

mass

vector, mass of peaks to label.

massTolerance

double, maximal deviation of a peak position to be considered.

digits

integer, number of decimal places.

underline

logical, underline peak values?

verticalOffset

numeric, move label vertically.

adj

numeric, adjust text to the left, center, right and top, center, bottom; see text.

cex

numeric, font size, see par.

family

name of font family, see par.

...

arguments to be passed to text.

See Also

MassPeaks, plot,AbstractMassObject,missing-method

Examples

## load library
library("MALDIquant");

## create a MassPeaks object from scratch
p <- new("MassPeaks", mass=1:20, intensity=sample(x=100:10000, size=20), 
         metaData=list(name="unrealistic example"));

## plot peaks
plot(p);

## label the first 5 peaks
labelPeaks(p, index=1:5);

## label all peaks in mass range 15 to 20 
labelPeaks(p, mass=15:20, underline=FALSE);

## label highest peaks (top 5)
top5 <- intensity(p) %in% sort(intensity(p), decreasing=TRUE)[1:5];
labelPeaks(p, index=top5, col="red");